I have multiple pages with flow headers that have the some of the same content as the page content and in some cases the content header follows directly the flow header. http://cl.ly/image/0l1F0S2B3621

I've searched the forum and haven't found any way to remove it from the pdf.

Is there anything I could do? CSS or Javascript?

No, at the moment it is not possible to contextually remove content from the document based on what else appears on the same page.